Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the GI tract. Surgical resection remains the only curative treatment for GIST, and is also beneficial for patients with localized resectable recurrent GIST. Gene test is not only important for diagnosis of GIST, but also valuable for estimating the response of GIST to target drug therapy and the prognosis. Here, the authors address the progress in these issues.